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Last update on 25. Nov 2018 .
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Search and highlight sequence patterns

OCCURRENCE

ARB_EDIT4/View/Search

ARB_EDIT4/<extended top area>/<search fields and buttons>

 

DESCRIPTION

ARB_EDIT4 supports searching and highlighting sequence patterns.

It supports 9 different pattern types, which will each be displayed in it's own color. Pattern types are e.g. "User1", "Probe", "Primer (global)", ...

Basic controls for each search pattern are available in the extended top-area of ARB_EDIT4 (to extend the top-area click the 'MORE' button): there you may jump to the next/previous occurrence of each pattern type, toggle pattern type display and open the detailed search parameter dialog for each pattern type.

 

Detailed search parameters (one window for each pattern type)

Search patterns

In the text field you can enter multiple search patterns. Different patterns are separated by newlines or commas.
'?' is treated as single letter wildcard
'#' is an end-of-line comment
Text written behind # will not be used for search. Instead this text will be displayed in the message window when you position your cursor on a found pattern.

Mark species with matches

Marks all species that match any of the current search patterns (does not change marks of any other species).

Last/Next

Jumps to the last/next occurrence of any of the given patterns. You can repeat your last search by pressing <CTRL-S> while focus is inside sequence view.
In the extended top-area of ARB_EDIT4 there are global NEXT/LAST buttons. They jump to the next match of ANY of all 9 pattern types.

Show?

If checked, the found parts are shown in different background colors (defined at Properties/Data Search)
See NOTES below for overlap priority.

Open folded?

If checked, the Last/Next-Button will open folded groups, to jump to the next occurrence. Otherwise search will jump over folded groups.

Auto jump?

If checked, the cursor will automatically jump to the nearest occurrence, if you change the search pattern or other search parameters.

Ignore gaps in sequence?

If checked, gaps in sequence will be ignored. (ACGU will find A-CG-U, AC---GU, ...)

Ignore gaps in pattern?

If checked, gaps in the search pattern will be ignored. (A-CG-U, AC---GU, ... will find ACGU)

Treat T and U as match?

If checked, T and U will be treated as equal. (ACGU will find ACGT and vice versa)

Ignore case?

If checked, a and A, c and C, ... are treated as equal (aCGu will find ACGU, AcgU, acgu, ...)

Search for complement?

If checked, search will go as well for complemented patterns.

Search for reverse?

If checked, search will go as well for reversed patterns.

Exact!

If checked, search will only go for the given combination of 'complement' and 'reverse'.
Example: If 'Exact', 'complement' and 'reverse' are checked,
         search will go only for complemented AND reversed
         patterns.

Allowed mismatches

Defines the minimum and maximum allowed number of non-matching base characters.
 

Store/restore search patterns

There are two ways to store/restore search patterns:


The latter is obsoleted and is only supported for compatibility.

Both store/restore all search parameters described above and both provide the possibility to exchange the search parameters between databases/users by saving/loading them to/from files and to move search parameters between different pattern types.

 

NOTES

Highlighted search patterns are drawn on top of other conditions determining background color (see ´Sequence background color priority´).

If the results from different pattern types overlap, patterns are prioritized as listed in the 'View/Search' submenu, i.e. "User1" is painted above "Primer (global)" and hence parts of the latter may be invisible.

The hits may also be highlighted in ARB_SECEDIT (see ´SECEDIT display options´).

 

EXAMPLES

None

 

WARNINGS

None

 

BUGS

No bugs known